Added center and testIntercept options to makeModels() as well as some checks. preprocessCoverage() now calculates the mean coverage at each base (before transformations). calculatePvalues(): P-values are now calculated by area and are only calculated if there is a null region or more. Renamed group to testvars in makeModels() so groupInfo in plotRegion() can be correctly differentiated. Added analyzeChr() and mergeResults() which are high level wrappers. Note that mergeRegions() calculates pooled p-values (and q-values) using the information from all chromosomes.
Finished mergeResults() and fixed a typo in makeModels()